[English] 日本語
Yorodumi
- PDB-6dio: Structure of class II HMG-CoA reductase from Delftia acidovorans ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dio
TitleStructure of class II HMG-CoA reductase from Delftia acidovorans with NAD bound
Components3-hydroxy-3-methylglutaryl coenzyme A reductase
KeywordsOXIDOREDUCTASE / Mevalonate pathway
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / ergosterol biosynthetic process / isoprenoid biosynthetic process / peroxisomal membrane / nucleotide binding
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily ...Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile. / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / 3-hydroxy-3-methylglutaryl coenzyme A reductase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsRagwan, E.R. / Arai, E. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116029 United States
CitationJournal: Biochemistry / Year: 2018
Title: New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase.
Authors: Ragwan, E.R. / Arai, E. / Kung, Y.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,83747
Polymers135,5723
Non-polymers5,26544
Water16,574920
1
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97832
Polymers90,3822
Non-polymers3,59730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18480 Å2
ΔGint-98 kcal/mol
Surface area26460 Å2
MethodPISA
2
C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,71830
Polymers90,3822
Non-polymers3,33728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area19650 Å2
ΔGint-66 kcal/mol
Surface area28220 Å2
MethodPISA
3
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,67594
Polymers271,1456
Non-polymers10,53088
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
crystal symmetry operation6_664x-y+1,x+1,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area65460 Å2
ΔGint-292 kcal/mol
Surface area72280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.000, 113.000, 437.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-889-

HOH

21A-903-

HOH

31C-704-

HOH

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein 3-hydroxy-3-methylglutaryl coenzyme A reductase / HMG-CoA reductase


Mass: 45190.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia acidovorans (bacteria) / Gene: CHL79_09160 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A291JGB7, UniProt: A9BQX8*PLUS, hydroxymethylglutaryl-CoA reductase

-
Non-polymers , 5 types, 964 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, pH 5.0, 0.5 M ammonium sulfate, 0.6 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2018
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.14→98.86 Å / Num. obs: 92136 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.0976 / Net I/σ(I): 5.4
Reflection shellResolution: 2.14→2.22 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→97.861 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.43
RfactorNum. reflection% reflection
Rfree0.2389 4723 5.13 %
Rwork0.1905 --
obs0.193 92123 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.14→97.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 333 920 10338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079530
X-RAY DIFFRACTIONf_angle_d0.90512921
X-RAY DIFFRACTIONf_dihedral_angle_d11.7146304
X-RAY DIFFRACTIONf_chiral_restr0.051512
X-RAY DIFFRACTIONf_plane_restr0.0051682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.16430.34411460.29732840X-RAY DIFFRACTION100
2.1643-2.18980.35451520.2952857X-RAY DIFFRACTION100
2.1898-2.21650.31571460.29212883X-RAY DIFFRACTION100
2.2165-2.24460.34111610.2842822X-RAY DIFFRACTION100
2.2446-2.27410.35381550.28332890X-RAY DIFFRACTION100
2.2741-2.30520.33221800.28362856X-RAY DIFFRACTION100
2.3052-2.33820.33181590.26252821X-RAY DIFFRACTION100
2.3382-2.37310.27561620.26412857X-RAY DIFFRACTION100
2.3731-2.41020.29121550.24662880X-RAY DIFFRACTION100
2.4102-2.44970.31521630.23912882X-RAY DIFFRACTION100
2.4497-2.49190.29941440.23442837X-RAY DIFFRACTION100
2.4919-2.53720.32191540.22482889X-RAY DIFFRACTION100
2.5372-2.58610.28331320.22592899X-RAY DIFFRACTION100
2.5861-2.63880.26791610.21422866X-RAY DIFFRACTION100
2.6388-2.69620.26961720.20722896X-RAY DIFFRACTION100
2.6962-2.75890.24961550.18772885X-RAY DIFFRACTION100
2.7589-2.8280.25821470.19042915X-RAY DIFFRACTION100
2.828-2.90440.27391560.17982873X-RAY DIFFRACTION100
2.9044-2.98990.24031470.18822917X-RAY DIFFRACTION100
2.9899-3.08640.25261490.19272889X-RAY DIFFRACTION100
3.0864-3.19670.23061660.20682917X-RAY DIFFRACTION100
3.1967-3.32470.23121700.17182924X-RAY DIFFRACTION100
3.3247-3.4760.19281440.15762923X-RAY DIFFRACTION100
3.476-3.65930.21091590.15042939X-RAY DIFFRACTION100
3.6593-3.88860.18861550.13992951X-RAY DIFFRACTION100
3.8886-4.18880.16291690.13112953X-RAY DIFFRACTION100
4.1888-4.61040.15951600.11732978X-RAY DIFFRACTION100
4.6104-5.27740.16971560.13243014X-RAY DIFFRACTION100
5.2774-6.64880.20031660.17473078X-RAY DIFFRACTION100
6.6488-97.96330.20591820.1793269X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more